Blender is automatically selecting multiple vertices while not holding down shift, help?
At the top of the window you should see the select tool 'Mode' this indicates whether it should Replace, Extend, Subtract, Invert or Intersect the selection - presumably you have somehow changed the mode to Extend (add to the existing selection).

Note that as well as the selection tool in the tool shelf you can alternatively press B for a box select. This does not use the same selection mode and instead defaults to 'Extend' the selection - unless you hold Shift to indicate Subtract.